===== Reading Scaffold from component AGP =====
./test/scaffold_from_contig_WGS.agp2.0:
	WARNING: ignoring AGP version comment - version already set to 2

No errors, 1 warning.
  Count Code  Description
      1  w62  ignoring AGP version comment - version already set to X


Objects                : 23
- with single component: 13

Scaffolds              : 23
- with single component: 13

Components                   : 95 (W)
  orientation +              : 81
  orientation -              : 14
  orientation ? (formerly 0) :  0
  orientation na             :  0

Gaps                   : 72 (N)
- do not break scaffold: 72
  scaffold, linkage yes: 71
  contamination, linkage yes:  1
- break it, linkage no :  0

Linkage evidence:
  paired-ends       : 71
  proximity_ligation:  1

Object names         :  23
  EG1_scaffold[1..23]:  23

Component names             :  95
  AADB[02037551..02037645].1:  95

#Comment line count    : 7

===== Reading Chromosome from scaffold AGP =====
./test/chr_from_scaffold_WGS.agp2.0:
	WARNING: ignoring AGP version comment - version already set to 2

No errors, 1 warning.
  Count Code  Description
      1  w62  ignoring AGP version comment - version already set to X


Objects                :  1
- with single component:  0

Scaffolds              : 23
- with single component: 23

Components                   : 23 (W)
  orientation +              : 20
  orientation -              :  0
  orientation ? (formerly 0) :  3
  orientation na             :  0

Gaps                   : 24 (N)
- do not break scaffold:  0
- break it, linkage no : 24
	contig         : 21 (100% of N gaps have length=50000)
	centromere     :  1
	telomere       :  2 (100% of N gaps have length=10000)

Most frequent N gap_length (87.5% or 21 lines): 50000

Object names:  1
  chrY      :  1

Component names      :  23
  EG1_scaffold[1..23]:  23

#Comment line count    : 9
./test/chr_from_contig_BAC.agp2.0_bad_ver:
	WARNING: AGP version comment is invalid, expecting ##agp-version 1.1 or ##agp-version 2.0

./test/chr_from_contig_BAC.agp2.0_bad_ver:10:chr37	1	8000000	1	N	8000000	short_arm	no	na
	NOTE: assuming AGP version 2 since linkage evidence (column 9) is NOT empty
./test/chr_from_contig_BAC.agp2.0_bad_ver:11:chr37	8000001	8050000	2	N	50000	heterochromatin	no	na
	WARNING: two consequtive gap lines (e.g. a gap at the end of a scaffold, two non scaffold-breaking gaps, ...)
./test/chr_from_contig_BAC.agp2.0_bad_ver:12:chr37	8050001	9050000	3	N	1000000	centromere	no	na
	WARNING: two consequtive gap lines (e.g. a gap at the end of a scaffold, two non scaffold-breaking gaps, ...)

./test/chr_from_contig_BAC.agp2.0_bad_ver:23:chr37	10205086	10205208	14	N	123	scaffold	yes	paired-ends;unspecified
	ERROR, line skipped: invalid value for linkage_evidence (column 9) -- "unspecified" cannot be combined with other terms

./test/chr_from_contig_BAC.agp2.0_bad_ver:29:chr37	10702843	10702919	20	N	77	scaffold	yes	paired-ends;paired-ends
	WARNING: linkage evidence term paired-ends appears more than once

./test/chr_from_contig_BAC.agp2.0_bad_ver:33:chr37	10939269	10956946	24	N	17678	scaffold	yes	clone_contig;
	ERROR, line skipped: invalid value for linkage_evidence (column 9): 

2 errors, 4 warnings, 1 note.
  Count Code  Description
      2  e04  invalid value for X
      2  w33  two consequtive gap lines (e.g. a gap at the end of a scaffold, two non scaffold-breaking gaps, ...)
      1  w58  assuming AGP version X
      1  w61  AGP version comment is invalid, expecting ##agp-version 1.1 or ##agp-version 2.0
      1  w63  linkage evidence term X appears more than once

NOTE: 2 invalid lines were skipped (not subjected to all the checks, not included in most of the counts below).


Objects                :   2
- with single component:   0

Scaffolds              :  27
- with single component:  13

Components                   : 208 (W:95, F:80, A:18, D:15)
  orientation +              : 131
  orientation -              :  77
  orientation ? (formerly 0) :   0
  orientation na             :   0

Gaps                   : 125 (N:113, U:12)
- do not break scaffold:  94
  scaffold, linkage yes:  94
- break it, linkage no :  31
	contig         :  24 (100% of N gaps have length=50000)
	centromere     :   2 (100% of N gaps have length=1000000)
	short_arm      :   1
	heterochromatin:   1
	telomere       :   3

Most frequent N gap_length (22.1% or 25 lines): 50000

Linkage evidence:
  paired-ends :  77
  within_clone:  12
  clone_contig:   4
  unspecified :   1

Object names:  2
  chrY      :  1
  chr37     :  1

Component names             : 189
  AADB[02037551..02037645].1:  95
  AC[139190..170923].[1..5] :  94

#Comment line count    : 16